U2U CAML Query Builder

I recently installed and used the CAML Query Builder from U2U. It's a good tool but there was one gotcha - in the XML that is built, the query is nested in <Query></Query>, - alright so far and the tool returns results. Copy this and use it in the SPQuery object and all results are returned regardless of the query used !? Well by removing the <Query></Query> tags it resolves the issue.